rs9295924

Positions:

• chr6-30814584-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_130726.1(LINC00243):​n.334C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.222 in 456,756 control chromosomes in the GnomAD database, including 14,388 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.18 (3128 hom., cov: 31)
  • Exomes 𝑓: 0.24 (11260 hom.)
• Consequence: LINC00243 NR_130726.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.355

Genes affected

LINC00243 (HGNC:30956): (long intergenic non-protein coding RNA 243)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.423 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC00243	NR_130726.1	n.334C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00243	ENST00000419357.6	n.146-15812C>T		intron_variant, non_coding_transcript_variant		3
LINC00243	ENST00000399196.1	n.334C>T		non_coding_transcript_exon_variant	2/2	2

Frequencies

GnomAD3 genomes AF: 0.180 AC: 27228 AN: 151664 Hom.: 3123 Cov.: 31

Gnomad AFR AF: 0.0964

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.307

Gnomad ASJ AF: 0.325

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.382

Gnomad FIN AF: 0.155

Gnomad MID AF: 0.210

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.204

GnomAD3 exomes AF: 0.272 AC: 37856 AN: 138988 Hom.: 6334 AF XY: 0.274 AC XY: 20615 AN XY: 75116

Gnomad AFR exome AF: 0.0966

Gnomad AMR exome AF: 0.395

Gnomad ASJ exome AF: 0.330

Gnomad EAS exome AF: 0.435

Gnomad SAS exome AF: 0.388

Gnomad FIN exome AF: 0.173

Gnomad NFE exome AF: 0.168

Gnomad OTH exome AF: 0.234

GnomAD4 exome AF: 0.243 AC: 74002 AN: 304974 Hom.: 11260 Cov.: 0 AF XY: 0.254 AC XY: 44166 AN XY: 173592

Gnomad4 AFR exome AF: 0.103

Gnomad4 AMR exome AF: 0.398

Gnomad4 ASJ exome AF: 0.328

Gnomad4 EAS exome AF: 0.424

Gnomad4 SAS exome AF: 0.382

Gnomad4 FIN exome AF: 0.169

Gnomad4 NFE exome AF: 0.163

Gnomad4 OTH exome AF: 0.224

GnomAD4 genome AF: 0.180 AC: 27257 AN: 151782 Hom.: 3128 Cov.: 31 AF XY: 0.188 AC XY: 13921 AN XY: 74162

Gnomad4 AFR AF: 0.0966

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.325

Gnomad4 EAS AF: 0.438

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.155

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.206

Alfa AF: 0.176 Hom.: 1951

Bravo AF: 0.186

Asia WGS AF: 0.393 AC: 1369 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.5
DANN	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9295924; hg19: chr6-30782361;